Evaluating Variant Calling Tools for Non-Matched Next-Generation Sequencing Data

Overview

Journal Sci Rep

Specialty Science

Date 2017 Feb 25

PMID 28233799

Citations 103

Authors

Sarah Sandmann

Aniek O de Graaf

Mohsen Karimi

Bert A van der Reijden

Eva Hellstrom-Lindberg

Joop H Jansen

Martin Dugas

Affiliations

Soon will be listed here.

Abstract

Valid variant calling results are crucial for the use of next-generation sequencing in clinical routine. However, there are numerous variant calling tools that usually differ in algorithms, filtering strategies, recommendations and thus, also in the output. We evaluated eight open-source tools regarding their ability to call single nucleotide variants and short indels with allelic frequencies as low as 1% in non-matched next-generation sequencing data: GATK HaplotypeCaller, Platypus, VarScan, LoFreq, FreeBayes, SNVer, SAMtools and VarDict. We analysed two real datasets from patients with myelodysplastic syndrome, covering 54 Illumina HiSeq samples and 111 Illumina NextSeq samples. Mutations were validated by re-sequencing on the same platform, on a different platform and expert based review. In addition we considered two simulated datasets with varying coverage and error profiles, covering 50 samples each. In all cases an identical target region consisting of 19 genes (42,322 bp) was analysed. Altogether, no tool succeeded in calling all mutations. High sensitivity was always accompanied by low precision. Influence of varying coverages- and background noise on variant calling was generally low. Taking everything into account, VarDict performed best. However, our results indicate that there is a need to improve reproducibility of the results in the context of multithreading.

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References

Lai Z, Markovets A, Ahdesmaki M, Chapman B, Hofmann O, McEwen R . VarDict: a novel and versatile variant caller for next-generation sequencing in cancer research. Nucleic Acids Res. 2016; 44(11):e108. PMC: 4914105. DOI: 10.1093/nar/gkw227. View

Forbes S, Beare D, Gunasekaran P, Leung K, Bindal N, Boutselakis H . COSMIC: exploring the world's knowledge of somatic mutations in human cancer. Nucleic Acids Res. 2014; 43(Database issue):D805-11. PMC: 4383913. DOI: 10.1093/nar/gku1075. View

Auton A, Brooks L, Durbin R, Garrison E, Kang H, Korbel J . A global reference for human genetic variation. Nature. 2015; 526(7571):68-74. PMC: 4750478. DOI: 10.1038/nature15393. View

Yeo Z, Wong J, Rozen S, Lee A . Evaluation and optimisation of indel detection workflows for ion torrent sequencing of the BRCA1 and BRCA2 genes. BMC Genomics. 2014; 15:516. PMC: 4079958. DOI: 10.1186/1471-2164-15-516. View

Bragg L, Stone G, Butler M, Hugenholtz P, Tyson G . Shining a light on dark sequencing: characterising errors in Ion Torrent PGM data. PLoS Comput Biol. 2013; 9(4):e1003031. PMC: 3623719. DOI: 10.1371/journal.pcbi.1003031. View

Loman N, Misra R, Dallman T, Constantinidou C, Gharbia S, Wain J . Performance comparison of benchtop high-throughput sequencing platforms. Nat Biotechnol. 2012; 30(5):434-9. DOI: 10.1038/nbt.2198. View

Mohamed S, Penaranda G, Gonzalez D, Camus C, Khiri H, Boulme R . Comparison of ultra-deep versus Sanger sequencing detection of minority mutations on the HIV-1 drug resistance interpretations after virological failure. AIDS. 2014; 28(9):1315-24. DOI: 10.1097/QAD.0000000000000267. View

Bao R, Huang L, Andrade J, Tan W, Kibbe W, Jiang H . Review of current methods, applications, and data management for the bioinformatics analysis of whole exome sequencing. Cancer Inform. 2014; 13(Suppl 2):67-82. PMC: 4179624. DOI: 10.4137/CIN.S13779. View

Alioto T, Buchhalter I, Derdak S, Hutter B, Eldridge M, Hovig E . A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing. Nat Commun. 2015; 6:10001. PMC: 4682041. DOI: 10.1038/ncomms10001. View

10.

Koboldt D, Zhang Q, Larson D, Shen D, McLellan M, Lin L . VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Res. 2012; 22(3):568-76. PMC: 3290792. DOI: 10.1101/gr.129684.111. View

11.

Sherry S, Ward M, Kholodov M, Baker J, Phan L, Smigielski E . dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2000; 29(1):308-11. PMC: 29783. DOI: 10.1093/nar/29.1.308. View

12.

Ewing A, Houlahan K, Hu Y, Ellrott K, Caloian C, Yamaguchi T . Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection. Nat Methods. 2015; 12(7):623-30. PMC: 4856034. DOI: 10.1038/nmeth.3407. View

13.

Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N . The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009; 25(16):2078-9. PMC: 2723002. DOI: 10.1093/bioinformatics/btp352. View

14.

Peifer M, Hertwig F, Roels F, Dreidax D, Gartlgruber M, Menon R . Telomerase activation by genomic rearrangements in high-risk neuroblastoma. Nature. 2015; 526(7575):700-4. PMC: 4881306. DOI: 10.1038/nature14980. View

15.

Choi Y, Sims G, Murphy S, Miller J, Chan A . Predicting the functional effect of amino acid substitutions and indels. PLoS One. 2012; 7(10):e46688. PMC: 3466303. DOI: 10.1371/journal.pone.0046688. View

16.

Rimmer A, Phan H, Mathieson I, Iqbal Z, Twigg S, Wilkie A . Integrating mapping-, assembly- and haplotype-based approaches for calling variants in clinical sequencing applications. Nat Genet. 2014; 46(8):912-918. PMC: 4753679. DOI: 10.1038/ng.3036. View

17.

Laurie S, Fernandez-Callejo M, Marco-Sola S, Trotta J, Camps J, Chacon A . From Wet-Lab to Variations: Concordance and Speed of Bioinformatics Pipelines for Whole Genome and Whole Exome Sequencing. Hum Mutat. 2016; 37(12):1263-1271. PMC: 5129537. DOI: 10.1002/humu.23114. View

18.

SANGER F, Nicklen S, Coulson A . DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A. 1977; 74(12):5463-7. PMC: 431765. DOI: 10.1073/pnas.74.12.5463. View

19.

Rothberg J, Hinz W, Rearick T, Schultz J, Mileski W, Davey M . An integrated semiconductor device enabling non-optical genome sequencing. Nature. 2011; 475(7356):348-52. DOI: 10.1038/nature10242. View

20.

Lek M, Karczewski K, Minikel E, Samocha K, Banks E, Fennell T . Analysis of protein-coding genetic variation in 60,706 humans. Nature. 2016; 536(7616):285-91. PMC: 5018207. DOI: 10.1038/nature19057. View